[gmx-users] CHARMM-GUI files give error in Gromacs

[Justin Lemkul]

On 9/2/16 10:44 AM, Justin Lemkul wrote:
>
>
> On 9/2/16 10:43 AM, gozde ergin wrote:
>> Ok I understand. I did exactly same thing for another molecule (SDS) and
>> everything is working without any error.
>> But I do not know what should I do with cis-pinonic.
>>
>
> If you upload a tarball of all the GROMACS files provided by CHARMM-GUI, I will
> take a quick look.
>

Contact the CHARMM-GUI developers. The problem is that the parameters specific 
to the cis-pinonic acid present in lig/lig.prm have not been included when the 
force field was converted, so only parameters in the ligand that are taken from 
the parent force field are present.  So their conversion script has a bug.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================